Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007266.1 Corchorus capsularis cultivar CVL-1 contig07287, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 49541
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2951 original size:22 final size:19
Alignment explanation
Indices: 2922--2965 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 19
2912 TTATATCTGA
2922 ATAATAATAT-TAATA--T
1 ATAATAATATCTAATATTT
2938 AT-ATAATATCTAATATTT
1 ATAATAATATCTAATATTT
2956 ATAATAATAT
1 ATAATAATAT
2966 ATATGTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 7 0.29
16 7 0.29
18 3 0.12
19 7 0.29
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAATAATATCTAATATTT
Found at i:2964 original size:28 final size:29
Alignment explanation
Indices: 2914--2969 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
2904 TATTTACGTT
*
2914 ATATCTGAATAATAATATTAATATATATA
1 ATATCTGAATAATAATAATAATATATATA
* *
2943 ATATCT-AATATTTATAATAATATATAT
1 ATATCTGAATAATAATAATAATATATAT
2970 GTAAAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (29 bp):
ATATCTGAATAATAATAATAATATATATA
Found at i:2969 original size:16 final size:17
Alignment explanation
Indices: 2922--2966 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
2912 TTATATCTGA
2922 ATAATAATATTAATATAT
1 ATAATAATA-TAATATAT
* *
2940 ATAAT-ATCTAATATTT
1 ATAATAATATAATATAT
2956 ATAATAATATA
1 ATAATAATATA
2967 TATGTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 12 0.52
17 6 0.26
18 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAATAATATAATATAT
Found at i:13648 original size:65 final size:65
Alignment explanation
Indices: 13544--13673 Score: 233
Period size: 65 Copynumber: 2.0 Consensus size: 65
13534 CAGGACAGGC
* *
13544 GAAAGGCTCATGGGCCCTACGTGCACCCAGAAAAAGGCCCTTCCTTCTAATTTGTAGCGATGGGT
1 GAAAGGCTCATGGGCCCTACGTGCACCCACAAAAAGGCCCTTCCTTCTAATTTGTAACGATGGGT
*
13609 GAAAGGCTCATGGGCCCTACGTGCACCCACAAAATGGCCCTTCCTTCTAATTTGTAACGATGGGT
1 GAAAGGCTCATGGGCCCTACGTGCACCCACAAAAAGGCCCTTCCTTCTAATTTGTAACGATGGGT
13674 TTATGGGAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.24
Consensus pattern (65 bp):
GAAAGGCTCATGGGCCCTACGTGCACCCACAAAAAGGCCCTTCCTTCTAATTTGTAACGATGGGT
Found at i:18515 original size:58 final size:58
Alignment explanation
Indices: 18452--18562 Score: 213
Period size: 58 Copynumber: 1.9 Consensus size: 58
18442 TTGGCATCTG
18452 TATATTTCTTGTTTTGAATCTCATTATATTAAGAAAATAAATTGTAGTTATTTGAAAA
1 TATATTTCTTGTTTTGAATCTCATTATATTAAGAAAATAAATTGTAGTTATTTGAAAA
*
18510 TATATTTCTTGTTTTGAATCTCATTATATTAAGAAAATAGATTGTAGTTATTT
1 TATATTTCTTGTTTTGAATCTCATTATATTAAGAAAATAAATTGTAGTTATTT
18563 CTTCAGTAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (58 bp):
TATATTTCTTGTTTTGAATCTCATTATATTAAGAAAATAAATTGTAGTTATTTGAAAA
Found at i:27172 original size:27 final size:27
Alignment explanation
Indices: 27099--27173 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
27089 GCAGAATGTG
* *
27099 CCATCCGATCCTCCCAACGACGCTGCT
1 CCATCCGATCCTCCCAAGGATGCTGCT
* * *
27126 CCATCCGGTCCTCTCAAGGATTCTGCT
1 CCATCCGATCCTCCCAAGGATGCTGCT
*
27153 CCATCCGATCCTCCCGAGGAT
1 CCATCCGATCCTCCCAAGGAT
27174 ATCCCTTTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.17, C:0.43, G:0.17, T:0.23
Consensus pattern (27 bp):
CCATCCGATCCTCCCAAGGATGCTGCT
Found at i:33955 original size:360 final size:359
Alignment explanation
Indices: 33254--33975 Score: 1345
Period size: 360 Copynumber: 2.0 Consensus size: 359
33244 ACAAAACCCT
33254 AATCCACTTGTCCTTGATTGAAAAGTTGTCAAAAGTTTATCCAGGAAGGCCCAAATTCGAATTCA
1 AATCCACTTGTCCTTGATTGAAAAGTTGTCAAAAGTTTATCCAGGAAGGCCCAAATTCGAATTCA
* *
33319 AAGGCATGATTCGGCCTAGCTCTAATTTACGCAGTAAATGGGGCGGCCCAAATATATCTCACACA
66 AAGGCATGATTCGGCCTAGCCCTAATTTACGCAGTAAATGGGGCAGCCCAAATATATCTCACACA
33384 TAAATCACTTGATTCTCCACTAATTATGGAAAATTCATAATCTTCATAGCCAAATTAGGAGAAAT
131 TAAATCACTTGATTCTCCACTAATTATGGAAAATTCATAATCTTCATAGCCAAATTAGGAGAAAT
*
33449 CAAAGTCATAAATTTAAAGTCAAACTTCTTCTCCTAGTTGACTTTGGTTCAAGGTGGTTAAAATC
196 CAAAGTCATAAATTCAAAGTCAAACTTCTTCTCCTAGTTGACTTTGGTTCAAGGTGGTTAAAATC
* * *
33514 CACTTTTACTTGGGGAAACTAATATAAATCTGAGGCCTTGATCTTTTAGCAATATGTGCATTTAC
261 CACTTTTACTTGGGGAAACTAATATAAATCTGAGCCCATGATCTTGTAGCAATATGTGCATTTAC
33579 CTAATTACCCAAAAATGTAAATTAGGGTATAGAC
326 CTAATTACCCAAAAATGTAAATTAGGGTATAGAC
*
33613 AATCCACTTGTCCTTGATTGAAAAGTTGTCAAAATTTTATCCCAGGAAGGCCCAAATTCGAATTC
1 AATCCACTTGTCCTTGATTGAAAAGTTGTCAAAAGTTTAT-CCAGGAAGGCCCAAATTCGAATTC
*
33678 AAAGGCATGATTCGGCCTAGCCCTAATTTACGCAGTAAATGGGGTAGCCCAAATATATCTCACAC
65 AAAGGCATGATTCGGCCTAGCCCTAATTTACGCAGTAAATGGGGCAGCCCAAATATATCTCACAC
33743 ATAAATCACTTGATTCTCCACTAATTATGGAAAATTCATAATCTTCATAGCCAAATTAGGAGAAA
130 ATAAATCACTTGATTCTCCACTAATTATGGAAAATTCATAATCTTCATAGCCAAATTAGGAGAAA
*
33808 TCAAAGTCATAAATTCGAAGTCAAACTTCTTCTCCTAGTTGACTTTGGTTCAAGGTGGTTAAAAT
195 TCAAAGTCATAAATTCAAAGTCAAACTTCTTCTCCTAGTTGACTTTGGTTCAAGGTGGTTAAAAT
*
33873 CCACTTTTACTTGGGGAAACTAATATAAATCTGAGCCCATGATCTTGTATCAATATGTGCATTTA
260 CCACTTTTACTTGGGGAAACTAATATAAATCTGAGCCCATGATCTTGTAGCAATATGTGCATTTA
33938 CCTAATTACCCAAAAATGTAAATTAGGGTATAGAC
325 CCTAATTACCCAAAAATGTAAATTAGGGTATAGAC
33973 AAT
1 AAT
33976 GCCCCCTATT
Statistics
Matches: 352, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
359 39 0.11
360 313 0.89
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (359 bp):
AATCCACTTGTCCTTGATTGAAAAGTTGTCAAAAGTTTATCCAGGAAGGCCCAAATTCGAATTCA
AAGGCATGATTCGGCCTAGCCCTAATTTACGCAGTAAATGGGGCAGCCCAAATATATCTCACACA
TAAATCACTTGATTCTCCACTAATTATGGAAAATTCATAATCTTCATAGCCAAATTAGGAGAAAT
CAAAGTCATAAATTCAAAGTCAAACTTCTTCTCCTAGTTGACTTTGGTTCAAGGTGGTTAAAATC
CACTTTTACTTGGGGAAACTAATATAAATCTGAGCCCATGATCTTGTAGCAATATGTGCATTTAC
CTAATTACCCAAAAATGTAAATTAGGGTATAGAC
Found at i:42312 original size:17 final size:16
Alignment explanation
Indices: 42290--42324 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
42280 TTTTTAAAGA
*
42290 TTTTCAAAATTTTTCGC
1 TTTTCAAAACTTTT-GC
42307 TTTTCAAAACTTTTGC
1 TTTTCAAAACTTTTGC
42323 TT
1 TT
42325 CTCTAGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (16 bp):
TTTTCAAAACTTTTGC
Found at i:46318 original size:19 final size:19
Alignment explanation
Indices: 46294--46332 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
46284 ATTTTATTGG
46294 TTATGACCTATGTTGTCTT
1 TTATGACCTATGTTGTCTT
*
46313 TTATGACCTCTGTTGTCTT
1 TTATGACCTATGTTGTCTT
46332 T
1 T
46333 CATTGAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.13, C:0.18, G:0.15, T:0.54
Consensus pattern (19 bp):
TTATGACCTATGTTGTCTT
Found at i:48177 original size:31 final size:33
Alignment explanation
Indices: 48141--48228 Score: 99
Period size: 36 Copynumber: 2.6 Consensus size: 33
48131 TTAATACTTT
* *
48141 CCACTGTTATTAAACTCTTTT-A-ATTAAGGCC
1 CCACTGTTATTAGACTCTTTTCAGACTAAGGCC
48172 CCACTGTTATTAGACTATCTTGTTCAGACTAAGGCC
1 CCACTGTTATTAGAC--TCTT-TTCAGACTAAGGCC
* *
48208 CCATTGTTATTAGAGTCTTTT
1 CCACTGTTATTAGACTCTTTT
48229 GTTTAGACTC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
31 14 0.29
33 6 0.12
34 6 0.12
35 1 0.02
36 21 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (33 bp):
CCACTGTTATTAGACTCTTTTCAGACTAAGGCC
Found at i:48609 original size:28 final size:29
Alignment explanation
Indices: 48559--48614 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
48549 ACGTGGATTT
* * *
48559 TCCATGTCAGCAATTAGT-GGGCCATATA
1 TCCACGTCAGCAATTAATAGGCCCATATA
*
48587 TCCACGTCAGCATTTAATAGGCCCATAT
1 TCCACGTCAGCAATTAATAGGCCCATAT
48615 GTGGAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (29 bp):
TCCACGTCAGCAATTAATAGGCCCATATA
Found at i:48761 original size:26 final size:28
Alignment explanation
Indices: 48725--48793 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 28
48715 AAGAGTCCAG
*
48725 CAAGAACAAAATT-ACAAC-AATTTAAC
1 CAAGAAAAAAATTAACAACAAATTTAAC
* *
48751 CAAGAAAAAAATTGCAACACCAAATTTAGC
1 CAAGAAAAAAATT--AACAACAAATTTAAC
48781 CAAGAAAAAAATT
1 CAAGAAAAAAATT
48794 GCGGCACTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 12 0.33
29 4 0.11
30 20 0.56
ACGTcount: A:0.58, C:0.17, G:0.07, T:0.17
Consensus pattern (28 bp):
CAAGAAAAAAATTAACAACAAATTTAAC
Found at i:49500 original size:2 final size:2
Alignment explanation
Indices: 49493--49541 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
49483 AAAGAAAAGG
49493 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
49535 GA GA GA G
1 GA GA GA G
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.